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BMRB: 15462

2JUZ

Solution NMR Structure of HI0947 from Haemophilus influenzae, Northeast Structural Genomics Consortium Target IR123

Authors

Ding, K., Ramelot, T.A., Cort, J.R., Wang, D., Nwosu, C., Owens, L., Xiao, R., Liu, J., Baran, M.C., Swapna, G.V T., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A.

Assembly

HI0947 Homodimer

Entity

1. HI0947 Homodimer (polymer, Thiol state: all free), 160 monomers, 17479.73 × 2 Da Detail

MAQHSKYSDA QLSAIVNDMI AVLEKHKAPV DLSLIALGNM ASNLLTTSVP QTQCEALAQA FSNSLINAVK TRLEHHHHHH MAQHSKYSDA QLSAIVNDMI AVLEKHKAPV DLSLIALGNM ASNLLTTSVP QTQCEALAQA FSNSLINAVK TRLEHHHHHH

Total weight

34959.46 Da

Max. entity weight

17479.73 Da

Source organism

Haemophilus influenzae

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 58.7 %, Completeness: 53.7 %, Completeness (bb): 55.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.7 % (966 of 1800)	53.7 % (494 of 920)	53.3 % (375 of 704)	55.1 % (97 of 176)
Backbone	55.5 % (528 of 952)	56.0 % (178 of 318)	55.0 % (263 of 478)	55.8 % (87 of 156)
Sidechain	52.4 % (527 of 1006)	52.5 % (316 of 602)	52.3 % (201 of 384)	50.0 % (10 of 20)
Aromatic	22.0 % (22 of 100)	22.0 % (11 of 50)	22.0 % (11 of 50)
Methyl	56.6 % (120 of 212)	55.7 % (59 of 106)	57.5 % (61 of 106)

1. HI0947

MAQHSKYSDA QLSAIVNDMI AVLEKHKAPV DLSLIALGNM ASNLLTTSVP QTQCEALAQA FSNSLINAVK TRLEHHHHHH MAQHSKYSDA QLSAIVNDMI AVLEKHKAPV DLSLIALGNM ASNLLTTSVP QTQCEALAQA FSNSLINAVK TRLEHHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
9	protein	[U-100% 13C; U-100% 15N]		0.66 mM
10	CaCl2	natural abundance		5 mM
11	NaCl	natural abundance		100 mM
12	NH4OAc	natural abundance		20 mM
13	DTT	natural abundance		10 mM
14	NaN3	natural abundance		0.02 %
15	D2O			100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2JUZ, Strand ID: A, B Detail

Release date

2007-10-15

Citation

Solution NMR Structure of HI0947 from Haemophilus influenzae
Ding, K., Ramelot, T.A., Cort, J.R., Wang, D., Nwosu, C., Owens, L., Xiao, R., Liu, J., Baran, M.C., Swapna, G.V T., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A.

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

3 2D 1H-13C Arom HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

4 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

8 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

12 3D 1H-13C Arom NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]		0.66 mM
2	CaCl2	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	NH4OAc	natural abundance		20 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %
7	H2O	natural abundance		95 %
8	D2O			5 %

13 4D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 5.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
9	protein	[U-100% 13C; U-100% 15N]		0.66 mM
10	CaCl2	natural abundance		5 mM
11	NaCl	natural abundance		100 mM
12	NH4OAc	natural abundance		20 mM
13	DTT	natural abundance		10 mM
14	NaN3	natural abundance		0.02 %
15	D2O			100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15462_2juz.nef
Input source #2: Coordindates	2juz.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80
MAQHSKYSDAQLSAIVNDMIAVLEKHKAPVDLSLIALGNMASNLLTTSVPQTQCEALAQAFSNSLINAVKTRLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAQHSKYSDAQLSAIVNDMIAVLEKHKAPVDLSLIALGNMASNLLTTSVPQTQCEALAQAFSNSLINAVKTRLEHHHHHH

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60--------70--------80
MAQHSKYSDAQLSAIVNDMIAVLEKHKAPVDLSLIALGNMASNLLTTSVPQTQCEALAQAFSNSLINAVKTRLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAQHSKYSDAQLSAIVNDMIAVLEKHKAPVDLSLIALGNMASNLLTTSVPQTQCEALAQAFSNSLINAVKTRLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	80	0	0	100.0
B	B	80	0	0	100.0

Content subtype: combined_15462_2juz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	853		98.8 (chain: A, length: 80)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1814 (1)	noe	86.3 (chain: A, length: 80), 86.3 (chain: B, length: 80)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	168 (1)	hbond	67.5 (chain: A, length: 80), 67.5 (chain: B, length: 80)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	220 (220)	.	77.5 (chain: A, length: 80), 77.5 (chain: B, length: 80)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 98.8%
- Total number of assignments
  - ¹H chemical shifts: 437
  - ¹³C chemical shifts: 330
  - ¹⁵N chemical shifts: 86
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 86.3%
  - Entity_assembly_ID: B, Chain length: 80, Sequence coverage: 86.3%
- Total number of restraints: 1812
- Weight of restraints: 1.0 (1812)
- Potential type of restraints: square-well-parabolic (1812)
- Range of distance target values: 2.65, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 67.5%
    - Entity_assembly_ID: B, Chain length: 80, Sequence coverage: 67.5%
  - Total number of restraints: 168
  - Weight of restraints: 1.0 (168)
  - Potential type of restraints: square-well-parabolic (168)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 77.5%
  - Entity_assembly_ID: B, Chain length: 80, Sequence coverage: 77.5%
- Total number of restraints: 220
- Total number of restraints per polymer type: 220
- Weight of restraints: 1.0 (220)
- Potential type of restraints: square-well-parabolic (220)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords homodimer, helix